I agree that it's confusing with the plus sign from the through-hole LED adjacent to the "backwards" LED.
My advice is to include detailed notes and even drawings of details like this, and actually almost anyplace orientation matters.
I had boards assembled with through-hole SIP networked resistors. It was obvious to me that the end of the resistor with the mark indicating the common pin should be positioned next to the triangle next to the footprint on the circuit board, but that detail wasn't obvious to the assembler who very consistently positioned both SIPS on every board the other way around.
That created a very strange error. One of the SIPS had pullup resistors for /MCLR (on the opposite end from the common pin), 2 switches and 2 option jumpers. I (stupidly) tested the boards without the option jumpers and everything worked perfectly. I installed one of the jumpers, and shipped the boards to my client.
When my client tried the boards, when he pressed the two switches simultaneously, the board would lock up, not even responding to the reset button. Turns out with the SIP the wrong way around, /MCLR was kind of at the wrong end of a voltage divider, and with 3 of the SIP resistors pulled low, the voltage level on /MCLR was in the disallowed range, hanging up the processor.